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MCL coexpression mm9:1039: Difference between revisions

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{{MCL_coexpression_mm9
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dehydrogenase activity;0.00807997794267702;56357!GO:0006573;valine metabolic process;0.00807997794267702;58875!GO:0008442;3-hydroxyisobutyrate dehydrogenase activity;0.00807997794267702;58875!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.00807997794267702;234309,58875!GO:0050662;coenzyme binding;0.00807997794267702;56357,58875!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.00807997794267702;234309,58875!GO:0004316;3-oxoacyl-[acyl-carrier-protein] reductase activity;0.00807997794267702;234309!GO:0009062;fatty acid catabolic process;0.00807997794267702;70025!GO:0016491;oxidoreductase activity;0.00874906374718147;56357,234309,58875!GO:0004616;phosphogluconate dehydrogenase (decarboxylating) activity;0.00887057747633578;58875!GO:0048037;cofactor binding;0.00887057747633578;56357,58875!GO:0005739;mitochondrion;0.0116250181027593;56357,83945,58875!GO:0004312;fatty-acid synthase activity;0.0124266493749851;234309!GO:0046395;carboxylic acid catabolic process;0.0129222992076651;70025!GO:0016054;organic acid catabolic process;0.0129222992076651;70025!GO:0009081;branched chain family amino acid metabolic process;0.0141322160224741;58875!GO:0006098;pentose-phosphate shunt;0.0143549637651335;58875!GO:0006740;NADPH regeneration;0.0143549637651335;58875!GO:0016290;palmitoyl-CoA hydrolase activity;0.0186930827713556;70025!GO:0005829;cytosol;0.0190751224128284;83945,70025!GO:0044444;cytoplasmic part;0.0190751224128284;56357,83945,70025,58875!GO:0016291;acyl-CoA thioesterase activity;0.0190751224128284;70025!GO:0006739;NADP metabolic process;0.0196471368667866;58875!GO:0003995;acyl-CoA dehydrogenase activity;0.0206530341095781;56357!GO:0016289;CoA hydrolase activity;0.0206530341095781;70025!GO:0044248;cellular catabolic process;0.021631562070282;70025,58875!GO:0019752;carboxylic acid metabolic process;0.0236493803871915;70025,58875!GO:0006082;organic acid metabolic 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|gostat_on_MCL_coexpression=GO:0008470;isovaleryl-CoA dehydrogenase activity;0.00807997794267702;56357!GO:0006573;valine metabolic process;0.00807997794267702;58875!GO:0008442;3-hydroxyisobutyrate dehydrogenase activity;0.00807997794267702;58875!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.00807997794267702;234309,58875!GO:0050662;coenzyme binding;0.00807997794267702;56357,58875!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.00807997794267702;234309,58875!GO:0004316;3-oxoacyl-[acyl-carrier-protein] reductase activity;0.00807997794267702;234309!GO:0009062;fatty acid catabolic process;0.00807997794267702;70025!GO:0016491;oxidoreductase activity;0.00874906374718147;56357,234309,58875!GO:0004616;phosphogluconate dehydrogenase (decarboxylating) activity;0.00887057747633578;58875!GO:0048037;cofactor binding;0.00887057747633578;56357,58875!GO:0005739;mitochondrion;0.0116250181027593;56357,83945,58875!GO:0004312;fatty-acid synthase activity;0.0124266493749851;234309!GO:0046395;carboxylic acid catabolic process;0.0129222992076651;70025!GO:0016054;organic acid catabolic process;0.0129222992076651;70025!GO:0009081;branched chain family amino acid metabolic process;0.0141322160224741;58875!GO:0006098;pentose-phosphate shunt;0.0143549637651335;58875!GO:0006740;NADPH regeneration;0.0143549637651335;58875!GO:0016290;palmitoyl-CoA hydrolase activity;0.0186930827713556;70025!GO:0005829;cytosol;0.0190751224128284;83945,70025!GO:0044444;cytoplasmic part;0.0190751224128284;56357,83945,70025,58875!GO:0016291;acyl-CoA thioesterase activity;0.0190751224128284;70025!GO:0006739;NADP metabolic process;0.0196471368667866;58875!GO:0003995;acyl-CoA dehydrogenase activity;0.0206530341095781;56357!GO:0016289;CoA hydrolase activity;0.0206530341095781;70025!GO:0044248;cellular catabolic process;0.021631562070282;70025,58875!GO:0019752;carboxylic acid metabolic process;0.0236493803871915;70025,58875!GO:0006082;organic acid metabolic process;0.0236493803871915;70025,58875!GO:0051287;NAD binding;0.0236493803871915;58875!GO:0006769;nicotinamide metabolic process;0.0236493803871915;58875!GO:0019362;pyridine nucleotide metabolic process;0.0249616164641196;58875!GO:0044242;cellular lipid catabolic process;0.0279736970247396;70025!GO:0009056;catabolic process;0.0279736970247396;70025,58875!GO:0006733;oxidoreduction coenzyme metabolic process;0.0303189034023962;58875!GO:0006767;water-soluble vitamin metabolic process;0.0358678919018525;58875!GO:0016627;oxidoreductase activity, acting on the CH-CH group of donors;0.0375416456033633;56357!GO:0031072;heat shock protein binding;0.0417177120662889;83945!GO:0006007;glucose catabolic process;0.0425852196503891;58875!GO:0046365;monosaccharide catabolic process;0.0425852196503891;58875!GO:0019320;hexose catabolic process;0.0425852196503891;58875!GO:0046164;alcohol catabolic process;0.0438838185182793;58875!GO:0051082;unfolded protein binding;0.0440697942513917;83945!GO:0050660;FAD binding;0.0440697942513917;56357!GO:0006766;vitamin metabolic process;0.0452432408623376;58875!GO:0044275;cellular carbohydrate catabolic process;0.0470712521752496;58875!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!2.02e-09!47;UBERON:0002365!6.99e-08!25;UBERON:0002330!6.99e-08!25;UBERON:0009854!3.62e-07!23;UBERON:0009856!3.62e-07!23;UBERON:0002107!5.93e-07!22;UBERON:0007499!5.93e-07!22;UBERON:0006925!5.93e-07!22;UBERON:0009497!5.93e-07!22;UBERON:0000015!5.93e-07!22;UBERON:0002423!5.93e-07!22;UBERON:0006235!5.93e-07!22;UBERON:0008835!5.93e-07!22;UBERON:0003894!5.93e-07!22;UBERON:0004161!5.93e-07!22;UBERON:0008836!5.93e-07!22
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,0.480627,0.810002,0.495263,0.587291,0.206208,0.616096,0.0609112,1.34037,0.575086,0.59526,1.46059,0.315771,0,0.795315,0.291368,0.561256,0.731589,0.374752,0.586604,0.598814,0.80655,1.07577,1.51917,0.184473,0.516511,0.911169,0.446946,0.50223,0.897561,0.289148,0.166577,0.316253,0.101236,0.766323,0.57142,0.258564,0.230656,0.800988,0.507468,0.258106,0.317766,0.515031,1.18381,0.714592,1.31862,0.0609361,0.347313,0.777641,0.654933,0.851157,1.04034,1.0579,1.47583,0.937475,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.611537,1.09164,0.507615,0.936963,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.613286,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,2.33242,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.187586,1.21618,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,2.00769,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,1.47713,0.147909,0.545091,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,1.98168,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,1.03935
|tfbs_overrepresentation_jaspar=MA0003.1;1.8002,MA0004.1;0.481116,MA0006.1;2.30634,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.694761,MA0017.1;0.337808,MA0019.1;1.753,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.0406078,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;1.90283,MA0061.1;2.05557,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.771749,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;4.19963e-05,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.0841779,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.0468,MA0103.1;0.348572,MA0105.1;1.5116,MA0106.1;0.677988,MA0107.1;0.906859,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.719313,MA0115.1;1.0246,MA0116.1;0.836994,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.964041,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;1.05551,MA0146.1;1.57153,MA0147.1;1.38091,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;1.37408,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.957645,MA0104.2;1.17226,MA0047.2;0.626803,MA0112.2;1.5617,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.397336,MA0155.1;0.336768,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.55478,MA0163.1;0.28052,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.16158,MA0102.2;1.65195,MA0258.1;1.27611,MA0259.1;1.34223,MA0442.1;0
}}

Latest revision as of 16:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:75398623..75398653,+p1@Chchd10
Mm9::chr16:4684099..4684137,+p1@Dnaja3
Mm9::chr2:118687722..118687744,+p1@Ivd
Mm9::chr2:118687745..118687758,+p2@Ivd
Mm9::chr4:151551921..151551936,+p3@Acot7
Mm9::chr6:52590241..52590253,-p2@Hibadh
Mm9::chr8:63966512..63966548,+p1@Cbr4


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0008470isovaleryl-CoA dehydrogenase activity0.00807997794267702
GO:0006573valine metabolic process0.00807997794267702
GO:00084423-hydroxyisobutyrate dehydrogenase activity0.00807997794267702
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.00807997794267702
GO:0050662coenzyme binding0.00807997794267702
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.00807997794267702
GO:00043163-oxoacyl-[acyl-carrier-protein] reductase activity0.00807997794267702
GO:0009062fatty acid catabolic process0.00807997794267702
GO:0016491oxidoreductase activity0.00874906374718147
GO:0004616phosphogluconate dehydrogenase (decarboxylating) activity0.00887057747633578
GO:0048037cofactor binding0.00887057747633578
GO:0005739mitochondrion0.0116250181027593
GO:0004312fatty-acid synthase activity0.0124266493749851
GO:0046395carboxylic acid catabolic process0.0129222992076651
GO:0016054organic acid catabolic process0.0129222992076651
GO:0009081branched chain family amino acid metabolic process0.0141322160224741
GO:0006098pentose-phosphate shunt0.0143549637651335
GO:0006740NADPH regeneration0.0143549637651335
GO:0016290palmitoyl-CoA hydrolase activity0.0186930827713556
GO:0005829cytosol0.0190751224128284
GO:0044444cytoplasmic part0.0190751224128284
GO:0016291acyl-CoA thioesterase activity0.0190751224128284
GO:0006739NADP metabolic process0.0196471368667866
GO:0003995acyl-CoA dehydrogenase activity0.0206530341095781
GO:0016289CoA hydrolase activity0.0206530341095781
GO:0044248cellular catabolic process0.021631562070282
GO:0019752carboxylic acid metabolic process0.0236493803871915
GO:0006082organic acid metabolic process0.0236493803871915
GO:0051287NAD binding0.0236493803871915
GO:0006769nicotinamide metabolic process0.0236493803871915
GO:0019362pyridine nucleotide metabolic process0.0249616164641196
GO:0044242cellular lipid catabolic process0.0279736970247396
GO:0009056catabolic process0.0279736970247396
GO:0006733oxidoreduction coenzyme metabolic process0.0303189034023962
GO:0006767water-soluble vitamin metabolic process0.0358678919018525
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0375416456033633
GO:0031072heat shock protein binding0.0417177120662889
GO:0006007glucose catabolic process0.0425852196503891
GO:0046365monosaccharide catabolic process0.0425852196503891
GO:0019320hexose catabolic process0.0425852196503891
GO:0046164alcohol catabolic process0.0438838185182793
GO:0051082unfolded protein binding0.0440697942513917
GO:0050660FAD binding0.0440697942513917
GO:0006766vitamin metabolic process0.0452432408623376
GO:0044275cellular carbohydrate catabolic process0.0470712521752496



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
epithelial tube2.02e-0947
exocrine gland6.99e-0825
exocrine system6.99e-0825
digestive tract diverticulum3.62e-0723
sac3.62e-0723
liver5.93e-0722
epithelial sac5.93e-0722
digestive gland5.93e-0722
epithelium of foregut-midgut junction5.93e-0722
anatomical boundary5.93e-0722
hepatobiliary system5.93e-0722
foregut-midgut junction5.93e-0722
hepatic diverticulum5.93e-0722
liver primordium5.93e-0722
septum transversum5.93e-0722
liver bud5.93e-0722


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.11.8002
MA0004.10.481116
MA0006.12.30634
MA0007.10.465969
MA0009.10.92425
MA0014.10.694761
MA0017.10.337808
MA0019.11.753
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.11.90283
MA0061.12.05557
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.14.19963e-05
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.11.5116
MA0106.10.677988
MA0107.10.906859
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.10.836994
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.964041
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.11.05551
MA0146.11.57153
MA0147.11.38091
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.21.37408
MA0138.20.727395
MA0002.20.205289
MA0137.20.957645
MA0104.21.17226
MA0047.20.626803
MA0112.21.5617
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.55478
MA0163.10.28052
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.16158
MA0102.21.65195
MA0258.11.27611
MA0259.11.34223
MA0442.10
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